<p>The Protestant Episcopal Church has been dipping the flag during the processional/recessional since the birth of the country (and still does). Christian religious services at USMA started out as Epsicopal and remained that way for some time. If the services at the Naval Academy started out as Episcopalian as they were for much of the 19th century at West Point, Im guessing the dipping of the flag during the services there stems from that era.</p>